… As a result, the form of the Chemscore function we use for protein–ligand docking is … docking
are not new concepts to protein–ligand docking. Consensus scoring is aimed at improving …

… Here, we propose a high-throughput protein-ligand complex MD simulation method to improve
docking results and more accurately distinguish binders from nonbinders. MD simulation …

… guide ligand binding in proteins—is a major hurdle in current protein–ligand docking efforts
… In this review the key concepts of protein–ligand docking methods are outlined, with major …

… protein-ligand docking and associated issues by focusing on: (a) where to find the protein
and the ligand … Nevertheless, the improvement in homology modelling methods has radically …

… within a set of true ligands requires still more accuracy in … a scoring function for docking a
ligand to a protein binding pocket. … improve relative to the reported performance of DOCK 4.0. …

… docking approach with reference blind docking runs over a set of 77 ligand-protein complexes
and 19 ligand-free proteins, we … : Is focused docking more accurate than blind docking? Is …

… docking and screening are limited. We describe a novel strategy to develop a reliable
protein–ligand … layers of contacts formed between protein residues and ligand atoms. In addition to …

… There is currently great interest in comparing protein–ligand docking programs. A review of
… starting ligand geometries and positions may have an appreciable effect on docking results. …

… can equally well be used in other docking and … improving scoring functions for protein-ligand
docking, our results indicate that improving the representation of the chemistry of proteins …

… of molecular docking is to reproduce the experimentally observed ″pose″ of the ligand in
… whether the inclusion of protein flexibility in a docking protocol would improve its utility as a ″…